Thanks for developing the super handy cpgwgs singularity which requires enormous effort and skills.
When doing the cpgwgs, a processing of a sample encountered an error at the cavemen flag step. The code we used is the singularity cpgwgs commands, and jobs for other samples has successfully completed, so I assume the parameters are all good.
in caveman/tmpCaveman/logs/Sanger_CGP_Caveman_Implement_caveman_flag.8.err
# .sh content. #
Can't use an undefined value as an ARRAY reference at \
/opt/wtsi-cgp/lib/perl5/Sanger/CGP/CavemanPostProcessor/PostProcessor.pm \
line 560, <__ANONIO__> line 3716.
at /opt/wtsi-cgp/bin/cgpFlagCaVEMan.pl line 125.
Command exited with non-zero status 2
63.01user 0.52system 1:03.87elapsed 99%CPU (0avgtext+0avgdata 134720maxresident)k
218384inputs+552outputs (0major+32965minor)pagefaults 0swaps
Same issue occurs to another sample at xxx.44.err for the processing of regions in chr15.
Dear developer,
Thanks for developing the super handy cpgwgs singularity which requires enormous effort and skills.
When doing the cpgwgs, a processing of a sample encountered an error at the cavemen flag step. The code we used is the singularity cpgwgs commands, and jobs for other samples has successfully completed, so I assume the parameters are all good.
in caveman/tmpCaveman/logs/Sanger_CGP_Caveman_Implement_caveman_flag.8.err
Same issue occurs to another sample at xxx.44.err for the processing of regions in chr15.
Thanks for any help or advice.